nesoni 0.124

Nesoni is a high-throughput sequencing data analysis toolset,which the VBC has developed to cope with the flood of Illumina, 454, and SOLiD data now being produced.

Our work is largely with bacterial genomes, and the design tradeoffs in nesoni reflect this.

Nesoni focusses on analysing the alignment of reads to a reference genome. Use of the SHRiMP and Bowtie2 read aligners is automated by nesoni. We use SHRiMP as it is able to detect small insertions and deletions in addition to SNPs. Output from other aligners may be imported in SAM format.

Nesoni can call a consensus of read alignments, taking care toindicate ambiguity. This can then be used in various ways: to determinethe protein level changes resulting from SNPs and indels, to find differences between multiple strains, or to produce n-way comparison data suitable for phylogenetic analysis in SplitsTree4.

~ Requirements==============

Python 2.7 or higher. Use of PyPy where possible is highly recommended for performance.